ChimeraX is not opened

[taehee.kim@…]

To Whom It May Concern,


I am facing a problem for several days, I cannot open the ChimeraX application.

I am using a MacBook, what's happened is, when I click the ChimeraX application, the icon of ChimeraX stays a few seconds on the Dock (at this moment it's still not opening), and it disappears. A few days before I had no problem to open the ChimeraX, it suddenly came up.

I have tried to reinstall it several times and also update a software of my MacBook, but still the ChimeraX is not opened..

Do you know what could be the reason? I would be grateful if you could suggest any solutions.

Thanks in advance.



Best,

Taehee Kim

[Eric Pettersen]

Hi Teehee,

Thanks for reporting this problem. It would be good to get more information about what is going wrong. Please try this:

1) In the Finder, go to your Applications Folder and navigate to its Utilities subfolder. In there there should be a Terminal application. Start the Terminal application, which will bring up a window with some text in it.
2) Now go to wherever you installed ChimeraX (usually the Applications folder) and right click on the ChimeraX icon. In the resulting popup menu choose "Show Package Contents". The Finder window will now show the usually-hidden Contents subfolder of the ChimeraX application. Navigate to its "bin" subfolder. In there there will be a "ChimeraX" file. Drag that file to the Terminal window and drop it. That will paste some text into the Terminal window (namely the file-system path to the ChimeraX file). Then in the Terminal window press the Return key. That will try to launch ChimeraX. Do any error messages appear there?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

Sorry Taehee, autocorrect changed your name to Teehee!

[taehee.kim@…]

Dear Eric,


I tried to open with Terminal, and there's seem to be some errors.

I have attached the text file. Please have a look.

If there're error, could you tell me how to solve this?

Thanks a lot!


Best,

Taehee

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, 15 April 2025 22:17:57
To: Kim, Taehee; pett@cgl.ucsf.edu
Subject: [+externe Mail+] Re: [ChimeraX] #17385: ChimeraX is not opened

#17385: ChimeraX is not opened
-----------------------------------+----------------------
          Reporter:  taehee.kim@…  |      Owner:  pett
              Type:  defect        |     Status:  accepted
          Priority:  normal        |  Milestone:
         Component:  Core          |    Version:
        Resolution:                |   Keywords:
        Blocked By:                |   Blocking:
Notify when closed:                |   Platform:  all
           Project:  ChimeraX      |
-----------------------------------+----------------------
Comment (by pett):

 Hi Teehee,
         Thanks for reporting this problem.  It would be good to get more
 information about what is going wrong.  Please try this:

         1) In the Finder, go to your Applications Folder and navigate to
 its Utilities subfolder.  In there there should be a Terminal application.
 Start the Terminal application, which will bring up a window with some
 text in it.
         2) Now go to wherever you installed ChimeraX (usually the
 Applications folder) and right click on the ChimeraX icon.  In the
 resulting popup menu choose "Show Package Contents".  The Finder window
 will now show the usually-hidden Contents subfolder of the ChimeraX
 application.  Navigate to its "bin" subfolder.  In there there will be a
 "ChimeraX" file.  Drag that file to the Terminal window and drop it.  That
 will paste some text into the Terminal window (namely the file-system path
 to the ChimeraX file).  Then in the Terminal window press the Return key.
 That will try to launch ChimeraX.  Do any error messages appear there?

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17385#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

Terminal Saved Output.txt​

[taehee.kim@…]

Added by email2trac

[Eric Pettersen]

Hi Taehee,

That information was helpful. In your ChimeraX Startup preferences you must have put /Users/gimtaehui/Desktop/태희/Chimera/kyte-doolittle_hydrophobicity.cxc as the value for the "Custom presets folder". Since that is a file and not a folder it causes ChimeraX to not startup properly. I have just now added code to safeguard against this, which will be available in the next daily build. You can fix the problem yourself by removing the .cxc file or by moving it elsewhere. ChimeraX already had a check for the file/folder not existing, but not for whether it actually was a folder and not a file.

--Eric